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GOanna 2.03
GOanna allows users to quickly add more GO annotations to their gene or gene product list by transferring GO annotations based on sequence homology.
GOanna is designed to be a special use case of BLAST, and normal BLAST rules about alignments and what constitutes a 'good' alignment apply.
Community rating: ?????
Quick Start
To use GOanna 2.02, import your data as either (1) a text list of protein accessions separated by a return/line break; or (2) a fasta file of either nucleotide or protein sequences.
Resources: http://www.agbase.msstate.edu/help/annahelp.htm
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> directory. |
Input File(s)
The input file is a text file containing either:
(1) protein accessions separated by a return/line break;
or
(2) a fasta file of either nucleotide or protein sequences.
Parameters Used in App
BLAST method: select BlastP for protein inputs or Blastx for nucleotide inputs.
Database: GOanna provides databases containing only sequences that have GO annotations.
Detailed information about the sequences contained in each database can be found here:
http://www.agbase.msstate.edu/help/GOanna_databases.htm
GOanna search database statistics can be found here:
http://www.agbase.msstate.edu/cgi-bin/agbase_species_blast_detail.pl
Please contact AgBase at agbase@hpc.msstate.edu to request customized databases.
Number of Alignments: This option restricts the number of reported alignments from the database. Only the alignments with the highest scores are reported.
Number of Descriptions: This option is used to select the number of short descriptions of matching sequences reported in the results.
Word-size: The BLAST program works by finding local alignments or 'words' matches between the query and database sequences and extending these matches. For blastp and blastx, non-exact word matches are extended. The amount of similarity can be varied so one normally uses just the word-sizes 2 and 3 for these searches.
Expect: This specifies the statistical significance threshold for reporting matches. The default value (10) means that 10 such matches are expected to be found merely by chance (Karlin and Altschul, 1990). Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported.
+Evidence Codes:+This feature lets you choose what types of GO evidence codes to return for the sequence matches. The GO Consortium recommends that if you are using BLAST to transfer GO from one sequence to another, you should only transfer "Experimental Evidence Codes". Experimental Evidence Codes(EXP,IDA,IPI,IMP,IGI,IEP) is set as default. More information about GO Evidence codes is available here:
http://www.geneontology.org/GO.evidence.shtml